#**Community diversity and composition at the haplotype, 3% and 5% lineages for each of the eight taxonomic orders studied**

#####This script gets all scripts of diversity using 8 arthropods order at multi-hierarchical levels 
#####We used 8 groups: Arachnda, Coleoptera, Collembola, Diptera, Hemiptera, Hymenoptera, Lepidoptera, and Myriapoda. 

library(stats)
library(base)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(tidyr)
library(knitr)
library(PMCMR)
## PMCMR is superseded by PMCMRplus and will be no longer maintained. You may wish to install PMCMRplus instead.
library(rcdd) 
## If you want correct answers, use rational arithmetic.
## See the Warnings sections added to help pages for
##     functions that do computational geometry.
library(vegan)
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.5-2
library(betapart) 
library(stringr)
library(permute)
library(lattice)


#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Diptera**
##Source to scripts Diptera and data
source("Diptera/Com_matrixes_data_exploration_Diptera_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 0.1705049 
## Run 1 stress 0.1742834 
## Run 2 stress 0.1706164 
## ... Procrustes: rmse 0.01675971  max resid 0.05041612 
## Run 3 stress 0.1728207 
## Run 4 stress 0.1700089 
## ... New best solution
## ... Procrustes: rmse 0.07444097  max resid 0.1745926 
## Run 5 stress 0.17832 
## Run 6 stress 0.1776025 
## Run 7 stress 0.1713384 
## Run 8 stress 0.1762392 
## Run 9 stress 0.1746584 
## Run 10 stress 0.1702322 
## ... Procrustes: rmse 0.05115378  max resid 0.2231485 
## Run 11 stress 0.173807 
## Run 12 stress 0.1757302 
## Run 13 stress 0.1769855 
## Run 14 stress 0.1739728 
## Run 15 stress 0.1746207 
## Run 16 stress 0.1767848 
## Run 17 stress 0.1786834 
## Run 18 stress 0.1742968 
## Run 19 stress 0.1758702 
## Run 20 stress 0.1786646 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Diptera/Com_matrixes_data_exploration_Diptera_3P_Site.R") 
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.212727 
## Run 1 stress 0.212727 
## ... Procrustes: rmse 0.0003655504  max resid 0.001477588 
## ... Similar to previous best
## Run 2 stress 0.2518546 
## Run 3 stress 0.2447956 
## Run 4 stress 0.2245212 
## Run 5 stress 0.2129618 
## ... Procrustes: rmse 0.006896282  max resid 0.03316547 
## Run 6 stress 0.232636 
## Run 7 stress 0.2379787 
## Run 8 stress 0.2188259 
## Run 9 stress 0.2127269 
## ... New best solution
## ... Procrustes: rmse 8.417947e-05  max resid 0.0003002356 
## ... Similar to previous best
## Run 10 stress 0.2197332 
## Run 11 stress 0.2199862 
## Run 12 stress 0.2389229 
## Run 13 stress 0.2225666 
## Run 14 stress 0.2127269 
## ... Procrustes: rmse 0.0002897773  max resid 0.001438204 
## ... Similar to previous best
## Run 15 stress 0.2245212 
## Run 16 stress 0.2129648 
## ... Procrustes: rmse 0.007687908  max resid 0.03785052 
## Run 17 stress 0.2502881 
## Run 18 stress 0.2199861 
## Run 19 stress 0.2127269 
## ... New best solution
## ... Procrustes: rmse 0.0001687952  max resid 0.0007165534 
## ... Similar to previous best
## Run 20 stress 0.2127272 
## ... Procrustes: rmse 0.0001697598  max resid 0.0006759932 
## ... Similar to previous best
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Diptera/Com_matrixes_data_exploration_Diptera_5P_Site.R") 
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.2150555 
## Run 1 stress 0.2150556 
## ... Procrustes: rmse 0.0001500731  max resid 0.0004548274 
## ... Similar to previous best
## Run 2 stress 0.2150555 
## ... Procrustes: rmse 8.383381e-05  max resid 0.0002804627 
## ... Similar to previous best
## Run 3 stress 0.2270005 
## Run 4 stress 0.2351285 
## Run 5 stress 0.2296127 
## Run 6 stress 0.2150555 
## ... Procrustes: rmse 6.604374e-05  max resid 0.0003030265 
## ... Similar to previous best
## Run 7 stress 0.2150555 
## ... Procrustes: rmse 4.966338e-05  max resid 0.000167786 
## ... Similar to previous best
## Run 8 stress 0.216303 
## Run 9 stress 0.2580705 
## Run 10 stress 0.2188767 
## Run 11 stress 0.2171952 
## Run 12 stress 0.2282902 
## Run 13 stress 0.2176331 
## Run 14 stress 0.2158436 
## Run 15 stress 0.2187359 
## Run 16 stress 0.2316618 
## Run 17 stress 0.2158436 
## Run 18 stress 0.2338777 
## Run 19 stress 0.2255358 
## Run 20 stress 0.2260855 
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Collembola**
##Source to scripts Collembola and data
source("Collembola/Com_matrixes_data_exploration_Collembola_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors

## Warning in Ops.factor(left, right): Expected 4 pieces. Additional pieces
## discarded in 42 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
## 16, 17, 18, 19, 20, ...].

## Warning in Ops.factor(left, right): Expected 4 pieces. Additional pieces
## discarded in 42 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
## 16, 17, 18, 19, 20, ...].

## Warning in Ops.factor(left, right): Expected 4 pieces. Additional pieces
## discarded in 42 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
## 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h_Collembola$sample_richness_Site_h, : Ties are present, p-
## values are not corrected.

## Run 0 stress 0.1042231 
## Run 1 stress 0.1043325 
## ... Procrustes: rmse 0.009088366  max resid 0.04961481 
## Run 2 stress 0.1043118 
## ... Procrustes: rmse 0.08305627  max resid 0.199973 
## Run 3 stress 0.1043253 
## ... Procrustes: rmse 0.008185306  max resid 0.04418749 
## Run 4 stress 0.1042262 
## ... Procrustes: rmse 0.00099368  max resid 0.005778975 
## ... Similar to previous best
## Run 5 stress 0.1043347 
## ... Procrustes: rmse 0.009319234  max resid 0.05099372 
## Run 6 stress 0.104336 
## ... Procrustes: rmse 0.08279228  max resid 0.2000422 
## Run 7 stress 0.1043367 
## ... Procrustes: rmse 0.08274708  max resid 0.2000752 
## Run 8 stress 0.1204174 
## Run 9 stress 0.1043097 
## ... Procrustes: rmse 0.08299686  max resid 0.2000107 
## Run 10 stress 0.1043095 
## ... Procrustes: rmse 0.08294348  max resid 0.200047 
## Run 11 stress 0.1043085 
## ... Procrustes: rmse 0.08288335  max resid 0.200116 
## Run 12 stress 0.1043326 
## ... Procrustes: rmse 0.009098066  max resid 0.04967263 
## Run 13 stress 0.1221812 
## Run 14 stress 0.10432 
## ... Procrustes: rmse 0.00732658  max resid 0.03897726 
## Run 15 stress 0.1043227 
## ... Procrustes: rmse 0.007779144  max resid 0.04173142 
## Run 16 stress 0.1042254 
## ... Procrustes: rmse 0.0008635217  max resid 0.005017736 
## ... Similar to previous best
## Run 17 stress 0.1181587 
## Run 18 stress 0.1043348 
## ... Procrustes: rmse 0.009253986  max resid 0.05059962 
## Run 19 stress 0.1043097 
## ... Procrustes: rmse 0.08299373  max resid 0.2000132 
## Run 20 stress 0.1216131 
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Collembola/Com_matrixes_data_exploration_Collembola_3P_Site.R") 
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03_Collembola$sample_richness_Site0.03, : Ties are present,
## p-values are not corrected.

## Run 0 stress 0.1037297 
## Run 1 stress 0.10641 
## Run 2 stress 0.109493 
## Run 3 stress 0.10641 
## Run 4 stress 0.1096296 
## Run 5 stress 0.1105657 
## Run 6 stress 0.1065262 
## Run 7 stress 0.108074 
## Run 8 stress 0.1089304 
## Run 9 stress 0.110051 
## Run 10 stress 0.1064129 
## Run 11 stress 0.1163356 
## Run 12 stress 0.1094158 
## Run 13 stress 0.1040404 
## ... Procrustes: rmse 0.01599745  max resid 0.09587982 
## Run 14 stress 0.1103509 
## Run 15 stress 0.1069449 
## Run 16 stress 0.1175932 
## Run 17 stress 0.1094139 
## Run 18 stress 0.1096315 
## Run 19 stress 0.1096867 
## Run 20 stress 0.103736 
## ... Procrustes: rmse 0.001806573  max resid 0.009240665 
## ... Similar to previous best
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Collembola/Com_matrixes_data_exploration_Collembola_5P_Site.R") 
## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

## Warning: Expected 4 pieces. Additional pieces discarded in 42 rows [1, 2,
## 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05_Collembola$sample_richness_Site0.05, : Ties are present,
## p-values are not corrected.

## Run 0 stress 0.1206288 
## Run 1 stress 0.1207496 
## ... Procrustes: rmse 0.06438135  max resid 0.212615 
## Run 2 stress 0.1247856 
## Run 3 stress 0.1281347 
## Run 4 stress 0.1242398 
## Run 5 stress 0.1249398 
## Run 6 stress 0.1244363 
## Run 7 stress 0.1235641 
## Run 8 stress 0.1300619 
## Run 9 stress 0.1207964 
## ... Procrustes: rmse 0.03218294  max resid 0.1662396 
## Run 10 stress 0.1255732 
## Run 11 stress 0.1206513 
## ... Procrustes: rmse 0.002323895  max resid 0.01086069 
## Run 12 stress 0.1273057 
## Run 13 stress 0.1209382 
## ... Procrustes: rmse 0.02715845  max resid 0.1659724 
## Run 14 stress 0.1243932 
## Run 15 stress 0.1205558 
## ... New best solution
## ... Procrustes: rmse 0.01577207  max resid 0.09109231 
## Run 16 stress 0.1257516 
## Run 17 stress 0.1207963 
## ... Procrustes: rmse 0.02818576  max resid 0.1680564 
## Run 18 stress 0.1228196 
## Run 19 stress 0.1244352 
## Run 20 stress 0.1249346 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Arachnida**
##Source to scripts Arachnida and data
source("Arachnida/Com_matrixes_data_exploration_Arachnida_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h_Arachnida$sample_richness_Site_h, : Ties are present, p-
## values are not corrected.

## Run 0 stress 0.1640223 
## Run 1 stress 0.1828367 
## Run 2 stress 0.1660367 
## Run 3 stress 0.1811127 
## Run 4 stress 0.1699014 
## Run 5 stress 0.1679739 
## Run 6 stress 0.1868526 
## Run 7 stress 0.1648388 
## Run 8 stress 0.1669304 
## Run 9 stress 0.1679123 
## Run 10 stress 0.1763698 
## Run 11 stress 0.1668807 
## Run 12 stress 0.166208 
## Run 13 stress 0.1674261 
## Run 14 stress 0.1800728 
## Run 15 stress 0.1758463 
## Run 16 stress 0.1674258 
## Run 17 stress 0.1809075 
## Run 18 stress 0.1705784 
## Run 19 stress 0.1738086 
## Run 20 stress 0.1762148 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Arachnida/Com_matrixes_data_exploration_Arachnida_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03_Arachnida$sample_richness_Site0.03, : Ties are present,
## p-values are not corrected.

## Run 0 stress 0.1922801 
## Run 1 stress 0.2020944 
## Run 2 stress 0.2005619 
## Run 3 stress 0.192182 
## ... New best solution
## ... Procrustes: rmse 0.01608043  max resid 0.06963253 
## Run 4 stress 0.1922696 
## ... Procrustes: rmse 0.008850614  max resid 0.04081894 
## Run 5 stress 0.1937838 
## Run 6 stress 0.1923497 
## ... Procrustes: rmse 0.01115861  max resid 0.0428627 
## Run 7 stress 0.2105356 
## Run 8 stress 0.1922794 
## ... Procrustes: rmse 0.01607519  max resid 0.06957806 
## Run 9 stress 0.1922817 
## ... Procrustes: rmse 0.01606974  max resid 0.0696413 
## Run 10 stress 0.1961158 
## Run 11 stress 0.1965957 
## Run 12 stress 0.1937838 
## Run 13 stress 0.196594 
## Run 14 stress 0.200564 
## Run 15 stress 0.1967166 
## Run 16 stress 0.1986574 
## Run 17 stress 0.1922698 
## ... Procrustes: rmse 0.008684918  max resid 0.0403805 
## Run 18 stress 0.1966405 
## Run 19 stress 0.1923329 
## ... Procrustes: rmse 0.01733909  max resid 0.06970682 
## Run 20 stress 0.2038669 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Arachnida/Com_matrixes_data_exploration_Arachnida_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05_Arachnida$sample_richness_Site0.05, : Ties are present,
## p-values are not corrected.

## Run 0 stress 0.199876 
## Run 1 stress 0.2087461 
## Run 2 stress 0.1998755 
## ... New best solution
## ... Procrustes: rmse 0.000164834  max resid 0.0008777296 
## ... Similar to previous best
## Run 3 stress 0.205641 
## Run 4 stress 0.2098513 
## Run 5 stress 0.1998764 
## ... Procrustes: rmse 0.0003774437  max resid 0.002133885 
## ... Similar to previous best
## Run 6 stress 0.2024718 
## Run 7 stress 0.2184258 
## Run 8 stress 0.2141527 
## Run 9 stress 0.1992423 
## ... New best solution
## ... Procrustes: rmse 0.02204456  max resid 0.08480384 
## Run 10 stress 0.2255285 
## Run 11 stress 0.1992462 
## ... Procrustes: rmse 0.003695492  max resid 0.01736026 
## Run 12 stress 0.213992 
## Run 13 stress 0.1998778 
## Run 14 stress 0.2081459 
## Run 15 stress 0.2103101 
## Run 16 stress 0.2256752 
## Run 17 stress 0.1998777 
## Run 18 stress 0.224641 
## Run 19 stress 0.211866 
## Run 20 stress 0.1992425 
## ... Procrustes: rmse 8.562322e-05  max resid 0.0002876852 
## ... Similar to previous best
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**We get the diversity analysis at haplotypes, C3% and 5% lineages in Hemiptera**
##Source to scripts Hemiptera and data
source("Hemiptera/Com_matrixes_data_exploration_Hemiptera_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 0.1232448 
## Run 1 stress 0.1302921 
## Run 2 stress 0.120326 
## ... New best solution
## ... Procrustes: rmse 0.05008299  max resid 0.1301977 
## Run 3 stress 0.1338129 
## Run 4 stress 0.1231923 
## Run 5 stress 0.1206297 
## ... Procrustes: rmse 0.0302274  max resid 0.08773975 
## Run 6 stress 0.1201466 
## ... New best solution
## ... Procrustes: rmse 0.02241538  max resid 0.08305554 
## Run 7 stress 0.1323811 
## Run 8 stress 0.1300975 
## Run 9 stress 0.1251024 
## Run 10 stress 0.1224937 
## Run 11 stress 0.1282869 
## Run 12 stress 0.1239621 
## Run 13 stress 0.1217274 
## Run 14 stress 0.1205673 
## ... Procrustes: rmse 0.04039636  max resid 0.1197719 
## Run 15 stress 0.1218062 
## Run 16 stress 0.1203239 
## ... Procrustes: rmse 0.02203384  max resid 0.08123151 
## Run 17 stress 0.1288358 
## Run 18 stress 0.1211859 
## Run 19 stress 0.1267372 
## Run 20 stress 0.1226463 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Hemiptera/Com_matrixes_data_exploration_Hemiptera_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.1638168 
## Run 1 stress 0.1690172 
## Run 2 stress 0.1674213 
## Run 3 stress 0.1662174 
## Run 4 stress 0.1679385 
## Run 5 stress 0.1726117 
## Run 6 stress 0.1679825 
## Run 7 stress 0.1727626 
## Run 8 stress 0.1664749 
## Run 9 stress 0.1665281 
## Run 10 stress 0.1661126 
## Run 11 stress 0.1657984 
## Run 12 stress 0.1717067 
## Run 13 stress 0.1672803 
## Run 14 stress 0.1698128 
## Run 15 stress 0.1658208 
## Run 16 stress 0.1712985 
## Run 17 stress 0.1707134 
## Run 18 stress 0.1671109 
## Run 19 stress 0.1677347 
## Run 20 stress 0.1688403 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Hemiptera/Com_matrixes_data_exploration_Hemiptera_5P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.1748273 
## Run 1 stress 0.1809059 
## Run 2 stress 0.1766329 
## Run 3 stress 0.1761215 
## Run 4 stress 0.1765299 
## Run 5 stress 0.1737685 
## ... New best solution
## ... Procrustes: rmse 0.06345736  max resid 0.1911859 
## Run 6 stress 0.176096 
## Run 7 stress 0.1809846 
## Run 8 stress 0.1752628 
## Run 9 stress 0.1750244 
## Run 10 stress 0.1844015 
## Run 11 stress 0.1743885 
## Run 12 stress 0.1752702 
## Run 13 stress 0.1819352 
## Run 14 stress 0.1789328 
## Run 15 stress 0.1754737 
## Run 16 stress 0.1775709 
## Run 17 stress 0.1828539 
## Run 18 stress 0.1744865 
## Run 19 stress 0.1764935 
## Run 20 stress 0.1766478 
## *** No convergence -- monoMDS stopping criteria:
##      2: no. of iterations >= maxit
##     18: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Hymenoptera**
##Source to scripts Hymenoptera and data
source("Hymenoptera/Com_matrixes_data_exploration_Hymenoptera_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 9.544494e-05 
## Run 1 stress 9.124703e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001032763  max resid 0.000222908 
## ... Similar to previous best
## Run 2 stress 9.58561e-05 
## ... Procrustes: rmse 6.953301e-05  max resid 0.0001774538 
## ... Similar to previous best
## Run 3 stress 9.90905e-05 
## ... Procrustes: rmse 8.437803e-05  max resid 0.0002251801 
## ... Similar to previous best
## Run 4 stress 9.593851e-05 
## ... Procrustes: rmse 7.433648e-05  max resid 0.0001542497 
## ... Similar to previous best
## Run 5 stress 7.873589e-05 
## ... New best solution
## ... Procrustes: rmse 9.706036e-05  max resid 0.000362411 
## ... Similar to previous best
## Run 6 stress 9.125645e-05 
## ... Procrustes: rmse 8.764146e-05  max resid 0.0002089603 
## ... Similar to previous best
## Run 7 stress 9.342967e-05 
## ... Procrustes: rmse 6.787735e-05  max resid 0.0001986684 
## ... Similar to previous best
## Run 8 stress 7.610741e-05 
## ... New best solution
## ... Procrustes: rmse 7.204226e-05  max resid 0.000337471 
## ... Similar to previous best
## Run 9 stress 8.648399e-05 
## ... Procrustes: rmse 7.135763e-05  max resid 0.0002847584 
## ... Similar to previous best
## Run 10 stress 8.962412e-05 
## ... Procrustes: rmse 7.045388e-05  max resid 0.0002541278 
## ... Similar to previous best
## Run 11 stress 9.905539e-05 
## ... Procrustes: rmse 7.877037e-05  max resid 0.0001868187 
## ... Similar to previous best
## Run 12 stress 8.928782e-05 
## ... Procrustes: rmse 8.783306e-05  max resid 0.0003403028 
## ... Similar to previous best
## Run 13 stress 9.109839e-05 
## ... Procrustes: rmse 8.596034e-05  max resid 0.0002847826 
## ... Similar to previous best
## Run 14 stress 9.233857e-05 
## ... Procrustes: rmse 7.720616e-05  max resid 0.0001478097 
## ... Similar to previous best
## Run 15 stress 9.986097e-05 
## ... Procrustes: rmse 7.797687e-05  max resid 0.0001909345 
## ... Similar to previous best
## Run 16 stress 8.946285e-05 
## ... Procrustes: rmse 7.865021e-05  max resid 0.0001611864 
## ... Similar to previous best
## Run 17 stress 9.13265e-05 
## ... Procrustes: rmse 7.104941e-05  max resid 0.0001676933 
## ... Similar to previous best
## Run 18 stress 9.553627e-05 
## ... Procrustes: rmse 8.913428e-05  max resid 0.0003027862 
## ... Similar to previous best
## Run 19 stress 9.43658e-05 
## ... Procrustes: rmse 7.132551e-05  max resid 0.0001743736 
## ... Similar to previous best
## Run 20 stress 9.743884e-05 
## ... Procrustes: rmse 5.242867e-05  max resid 0.0001410682 
## ... Similar to previous best
## *** Solution reached
## Warning in metaMDS(beta.pair$beta.sim): stress is (nearly) zero: you may
## have insufficient data
## species scores not available

## species scores not available

## Run 0 stress 0.1734477 
## Run 1 stress 0.1852592 
## Run 2 stress 0.1717926 
## ... New best solution
## ... Procrustes: rmse 0.08052484  max resid 0.2659881 
## Run 3 stress 0.1801441 
## Run 4 stress 0.1842457 
## Run 5 stress 0.1757073 
## Run 6 stress 0.177248 
## Run 7 stress 0.1760273 
## Run 8 stress 0.1818146 
## Run 9 stress 0.1773927 
## Run 10 stress 0.1725281 
## Run 11 stress 0.1789951 
## Run 12 stress 0.1775665 
## Run 13 stress 0.1723463 
## Run 14 stress 0.1757022 
## Run 15 stress 0.1788915 
## Run 16 stress 0.1753499 
## Run 17 stress 0.1707388 
## ... New best solution
## ... Procrustes: rmse 0.03237597  max resid 0.1090247 
## Run 18 stress 0.1855473 
## Run 19 stress 0.1747117 
## Run 20 stress 0.186251 
## *** No convergence -- monoMDS stopping criteria:
##      1: no. of iterations >= maxit
##     19: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Hymenoptera/Com_matrixes_data_exploration_Hymenoptera_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.22086 
## Run 1 stress 0.2212641 
## ... Procrustes: rmse 0.1159116  max resid 0.5053767 
## Run 2 stress 0.2508214 
## Run 3 stress 0.2215354 
## Run 4 stress 0.2703537 
## Run 5 stress 0.2316091 
## Run 6 stress 0.2202948 
## ... New best solution
## ... Procrustes: rmse 0.1129327  max resid 0.481907 
## Run 7 stress 0.2225233 
## Run 8 stress 0.2240296 
## Run 9 stress 0.2515532 
## Run 10 stress 0.2374314 
## Run 11 stress 0.2290868 
## Run 12 stress 0.2220561 
## Run 13 stress 0.2245914 
## Run 14 stress 0.2194369 
## ... New best solution
## ... Procrustes: rmse 0.01442216  max resid 0.04465484 
## Run 15 stress 0.2503353 
## Run 16 stress 0.2562257 
## Run 17 stress 0.2565169 
## Run 18 stress 0.2247513 
## Run 19 stress 0.2246353 
## Run 20 stress 0.2393523 
## *** No convergence -- monoMDS stopping criteria:
##      1: no. of iterations >= maxit
##     19: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Hymenoptera/Com_matrixes_data_exploration_Hymenoptera_5P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.2315232 
## Run 1 stress 0.2499491 
## Run 2 stress 0.2290739 
## ... New best solution
## ... Procrustes: rmse 0.1131764  max resid 0.4347482 
## Run 3 stress 0.2335993 
## Run 4 stress 0.2420133 
## Run 5 stress 0.2500365 
## Run 6 stress 0.2583728 
## Run 7 stress 0.2560814 
## Run 8 stress 0.240423 
## Run 9 stress 0.2196152 
## ... New best solution
## ... Procrustes: rmse 0.07547701  max resid 0.3049032 
## Run 10 stress 0.2536737 
## Run 11 stress 0.2186078 
## ... New best solution
## ... Procrustes: rmse 0.05526248  max resid 0.2483082 
## Run 12 stress 0.2375132 
## Run 13 stress 0.2197507 
## Run 14 stress 0.2406202 
## Run 15 stress 0.2187457 
## ... Procrustes: rmse 0.01125625  max resid 0.04777274 
## Run 16 stress 0.2201127 
## Run 17 stress 0.2316705 
## Run 18 stress 0.2228166 
## Run 19 stress 0.2197297 
## Run 20 stress 0.2396929 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Coleoptera**
##Source to scripts Coleoptera and data
source("Coleoptera/Com_matrixes_data_exploration_Coleoptera_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 9.552724e-05 
## Run 1 stress 9.692118e-05 
## ... Procrustes: rmse 0.0001430887  max resid 0.0003406894 
## ... Similar to previous best
## Run 2 stress 9.434765e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001218041  max resid 0.0004176262 
## ... Similar to previous best
## Run 3 stress 9.907821e-05 
## ... Procrustes: rmse 0.0001491776  max resid 0.0005699299 
## ... Similar to previous best
## Run 4 stress 9.49929e-05 
## ... Procrustes: rmse 0.0002059656  max resid 0.000637209 
## ... Similar to previous best
## Run 5 stress 9.588271e-05 
## ... Procrustes: rmse 0.0001982477  max resid 0.0004757986 
## ... Similar to previous best
## Run 6 stress 9.023621e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001112822  max resid 0.0002118612 
## ... Similar to previous best
## Run 7 stress 9.346549e-05 
## ... Procrustes: rmse 0.0001666722  max resid 0.0005003735 
## ... Similar to previous best
## Run 8 stress 9.49311e-05 
## ... Procrustes: rmse 0.0001174962  max resid 0.0002521223 
## ... Similar to previous best
## Run 9 stress 8.068841e-05 
## ... New best solution
## ... Procrustes: rmse 0.000167037  max resid 0.0004579998 
## ... Similar to previous best
## Run 10 stress 9.754579e-05 
## ... Procrustes: rmse 0.000208667  max resid 0.0005624697 
## ... Similar to previous best
## Run 11 stress 9.432962e-05 
## ... Procrustes: rmse 0.0001325474  max resid 0.0006154589 
## ... Similar to previous best
## Run 12 stress 9.613648e-05 
## ... Procrustes: rmse 0.0001156214  max resid 0.00033936 
## ... Similar to previous best
## Run 13 stress 9.574783e-05 
## ... Procrustes: rmse 0.000174489  max resid 0.0005932774 
## ... Similar to previous best
## Run 14 stress 9.739414e-05 
## ... Procrustes: rmse 9.54317e-05  max resid 0.0002297472 
## ... Similar to previous best
## Run 15 stress 9.184774e-05 
## ... Procrustes: rmse 7.365552e-05  max resid 0.0002484014 
## ... Similar to previous best
## Run 16 stress 8.726268e-05 
## ... Procrustes: rmse 0.0001293308  max resid 0.0006225199 
## ... Similar to previous best
## Run 17 stress 9.564366e-05 
## ... Procrustes: rmse 0.0002126053  max resid 0.0005995389 
## ... Similar to previous best
## Run 18 stress 9.70105e-05 
## ... Procrustes: rmse 0.0001296802  max resid 0.0005624632 
## ... Similar to previous best
## Run 19 stress 9.618529e-05 
## ... Procrustes: rmse 4.728994e-05  max resid 0.0001134518 
## ... Similar to previous best
## Run 20 stress 9.64537e-05 
## ... Procrustes: rmse 0.0001121901  max resid 0.0002655575 
## ... Similar to previous best
## *** Solution reached
## Warning in metaMDS(beta.pair$beta.sim): stress is (nearly) zero: you may
## have insufficient data
## species scores not available

## Run 0 stress 0.1016899 
## Run 1 stress 0.1160957 
## Run 2 stress 0.1166976 
## Run 3 stress 0.1108654 
## Run 4 stress 0.1077952 
## Run 5 stress 0.1186629 
## Run 6 stress 0.1112831 
## Run 7 stress 0.1128334 
## Run 8 stress 0.1087854 
## Run 9 stress 0.1046179 
## Run 10 stress 0.108274 
## Run 11 stress 0.1104088 
## Run 12 stress 0.1030868 
## Run 13 stress 0.1086193 
## Run 14 stress 0.1087196 
## Run 15 stress 0.1030807 
## Run 16 stress 0.1072223 
## Run 17 stress 0.1111447 
## Run 18 stress 0.108601 
## Run 19 stress 0.1073821 
## Run 20 stress 0.1158125 
## *** No convergence -- monoMDS stopping criteria:
##      2: no. of iterations >= maxit
##     18: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Coleoptera/Com_matrixes_data_exploration_Coleoptera_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.1296922 
## Run 1 stress 0.1270601 
## ... New best solution
## ... Procrustes: rmse 0.09587376  max resid 0.3105905 
## Run 2 stress 0.1320351 
## Run 3 stress 0.1287044 
## Run 4 stress 0.1346142 
## Run 5 stress 0.1237186 
## ... New best solution
## ... Procrustes: rmse 0.05551642  max resid 0.1596561 
## Run 6 stress 0.1363569 
## Run 7 stress 0.1366099 
## Run 8 stress 0.1410253 
## Run 9 stress 0.135464 
## Run 10 stress 0.1441057 
## Run 11 stress 0.126692 
## Run 12 stress 0.1242386 
## Run 13 stress 0.1306403 
## Run 14 stress 0.1355797 
## Run 15 stress 0.1311064 
## Run 16 stress 0.1373353 
## Run 17 stress 0.1257149 
## Run 18 stress 0.1354932 
## Run 19 stress 0.1375001 
## Run 20 stress 0.1375196 
## *** No convergence -- monoMDS stopping criteria:
##      7: no. of iterations >= maxit
##     13: stress ratio > sratmax
## species scores not available

## species scores not available

## Run 0 stress 0.1398926 
## Run 1 stress 0.1446353 
## Run 2 stress 0.144848 
## Run 3 stress 0.1452591 
## Run 4 stress 0.1426066 
## Run 5 stress 0.1469758 
## Run 6 stress 0.1336171 
## ... New best solution
## ... Procrustes: rmse 0.08465303  max resid 0.3204013 
## Run 7 stress 0.1468523 
## Run 8 stress 0.1422256 
## Run 9 stress 0.1416075 
## Run 10 stress 0.1328955 
## ... New best solution
## ... Procrustes: rmse 0.02123241  max resid 0.0541119 
## Run 11 stress 0.1471635 
## Run 12 stress 0.1484118 
## Run 13 stress 0.1441016 
## Run 14 stress 0.1470549 
## Run 15 stress 0.1499594 
## Run 16 stress 0.1498131 
## Run 17 stress 0.1472921 
## Run 18 stress 0.1472759 
## Run 19 stress 0.1471485 
## Run 20 stress 0.1345768 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Coleoptera/Com_matrixes_data_exploration_Coleoptera_5P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.1400952 
## Run 1 stress 0.1413643 
## Run 2 stress 0.1436179 
## Run 3 stress 0.1440866 
## Run 4 stress 0.1434918 
## Run 5 stress 0.1407486 
## Run 6 stress 0.1453467 
## Run 7 stress 0.1406028 
## Run 8 stress 0.1407293 
## Run 9 stress 0.1431137 
## Run 10 stress 0.1449251 
## Run 11 stress 0.1430277 
## Run 12 stress 0.1461916 
## Run 13 stress 0.1410899 
## Run 14 stress 0.1422352 
## Run 15 stress 0.1389715 
## ... New best solution
## ... Procrustes: rmse 0.07856614  max resid 0.2975092 
## Run 16 stress 0.141578 
## Run 17 stress 0.1420728 
## Run 18 stress 0.1438968 
## Run 19 stress 0.1399224 
## Run 20 stress 0.1418942 
## *** No convergence -- monoMDS stopping criteria:
##      7: no. of iterations >= maxit
##     13: stress ratio > sratmax
## species scores not available

## species scores not available

## Run 0 stress 0.1639448 
## Run 1 stress 0.1744695 
## Run 2 stress 0.1765964 
## Run 3 stress 0.1662604 
## Run 4 stress 0.1655517 
## Run 5 stress 0.1739224 
## Run 6 stress 0.1703355 
## Run 7 stress 0.165239 
## Run 8 stress 0.1753459 
## Run 9 stress 0.1672981 
## Run 10 stress 0.1768088 
## Run 11 stress 0.1756904 
## Run 12 stress 0.1685106 
## Run 13 stress 0.1673672 
## Run 14 stress 0.1673677 
## Run 15 stress 0.166511 
## Run 16 stress 0.1638376 
## ... New best solution
## ... Procrustes: rmse 0.05350718  max resid 0.2002146 
## Run 17 stress 0.16962 
## Run 18 stress 0.1713401 
## Run 19 stress 0.1647595 
## Run 20 stress 0.1641853 
## ... Procrustes: rmse 0.0559174  max resid 0.2217796 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Myriapoda**
##Source to scripts Myriapoda and data
source("Myriapoda/Com_matrixes_data_exploration_Myriapoda_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 0.004498111 
## Run 1 stress 0.008835104 
## Run 2 stress 0.008771117 
## Run 3 stress 0.004270409 
## ... New best solution
## ... Procrustes: rmse 0.1781292  max resid 0.3303976 
## Run 4 stress 0.01515644 
## Run 5 stress 0.004248592 
## ... New best solution
## ... Procrustes: rmse 0.1320902  max resid 0.3435172 
## Run 6 stress 0.003957574 
## ... New best solution
## ... Procrustes: rmse 0.107408  max resid 0.2391002 
## Run 7 stress 0.02375465 
## Run 8 stress 0.007871579 
## Run 9 stress 0.003903354 
## ... New best solution
## ... Procrustes: rmse 0.1313549  max resid 0.2596707 
## Run 10 stress 0.006257089 
## Run 11 stress 0.003866141 
## ... New best solution
## ... Procrustes: rmse 0.1345201  max resid 0.2196701 
## Run 12 stress 0.003861922 
## ... New best solution
## ... Procrustes: rmse 0.1441505  max resid 0.3306959 
## Run 13 stress 0.0311195 
## Run 14 stress 0.006142294 
## Run 15 stress 0.00403747 
## ... Procrustes: rmse 0.1178921  max resid 0.267503 
## Run 16 stress 0.009679839 
## Run 17 stress 0.004718485 
## Run 18 stress 0.003917166 
## ... Procrustes: rmse 0.1523682  max resid 0.3586479 
## Run 19 stress 0.004349284 
## ... Procrustes: rmse 0.1476007  max resid 0.3107432 
## Run 20 stress 0.02559551 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Myriapoda/Com_matrixes_data_exploration_Myriapoda_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.03791431 
## Run 1 stress 0.03565255 
## ... New best solution
## ... Procrustes: rmse 0.1858931  max resid 0.4179719 
## Run 2 stress 0.007639864 
## ... New best solution
## ... Procrustes: rmse 0.1651932  max resid 0.3139572 
## Run 3 stress 0.04387121 
## Run 4 stress 0.03802811 
## Run 5 stress 0.03461826 
## Run 6 stress 0.04120583 
## Run 7 stress 0.03938402 
## Run 8 stress 0.03651993 
## Run 9 stress 0.03931647 
## Run 10 stress 0.007655915 
## ... Procrustes: rmse 0.007121302  max resid 0.02997574 
## Run 11 stress 0.04842156 
## Run 12 stress 0.05042658 
## Run 13 stress 0.04225531 
## Run 14 stress 0.04611576 
## Run 15 stress 0.07827083 
## Run 16 stress 0.03277704 
## Run 17 stress 0.006114432 
## ... New best solution
## ... Procrustes: rmse 0.122026  max resid 0.2434565 
## Run 18 stress 0.05375811 
## Run 19 stress 0.03870693 
## Run 20 stress 0.04523618 
## *** No convergence -- monoMDS stopping criteria:
##     10: no. of iterations >= maxit
##     10: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Myriapoda/Com_matrixes_data_exploration_Myriapoda_5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.04673913 
## Run 1 stress 0.04586795 
## ... New best solution
## ... Procrustes: rmse 0.1039306  max resid 0.1882187 
## Run 2 stress 0.02858822 
## ... New best solution
## ... Procrustes: rmse 0.07512826  max resid 0.2726096 
## Run 3 stress 0.05968563 
## Run 4 stress 0.01451371 
## ... New best solution
## ... Procrustes: rmse 0.1453555  max resid 0.4224504 
## Run 5 stress 0.03385359 
## Run 6 stress 0.04316031 
## Run 7 stress 0.04511632 
## Run 8 stress 0.03180625 
## Run 9 stress 0.0517851 
## Run 10 stress 0.03461956 
## Run 11 stress 0.0317859 
## Run 12 stress 0.02636104 
## Run 13 stress 0.02639511 
## Run 14 stress 0.03425297 
## Run 15 stress 0.04441202 
## Run 16 stress 0.02906087 
## Run 17 stress 0.02859055 
## Run 18 stress 0.05359923 
## Run 19 stress 0.05079672 
## Run 20 stress 0.03171714 
## *** No convergence -- monoMDS stopping criteria:
##      9: no. of iterations >= maxit
##     11: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**We get the diversity analysis at haplotypes, 3% and 5% lineages in Lepidoptera#**
##Source to scripts Lepidoptera and data
source("Lepidoptera/Com_matrixes_data_exploration_Lepidoptera_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 0.02414004 
## Run 1 stress 0.05808426 
## Run 2 stress 0.03899857 
## Run 3 stress 0.04282035 
## Run 4 stress 0.03384725 
## Run 5 stress 0.03180344 
## Run 6 stress 0.04360861 
## Run 7 stress 0.01451009 
## ... New best solution
## ... Procrustes: rmse 0.08806015  max resid 0.2833596 
## Run 8 stress 0.03180352 
## Run 9 stress 0.03735259 
## Run 10 stress 0.03452066 
## Run 11 stress 0.02797805 
## Run 12 stress 0.01452828 
## ... Procrustes: rmse 0.02985246  max resid 0.1002764 
## Run 13 stress 0.02654015 
## Run 14 stress 0.04455215 
## Run 15 stress 0.04716167 
## Run 16 stress 0.04150023 
## Run 17 stress 0.04671479 
## Run 18 stress 0.04189623 
## Run 19 stress 0.0328243 
## Run 20 stress 0.0402562 
## *** No convergence -- monoMDS stopping criteria:
##      7: no. of iterations >= maxit
##     13: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Lepidoptera/Com_matrixes_data_exploration_Lepidoptera_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.03$sample_richness_Site0.03, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.04662604 
## Run 1 stress 0.03266709 
## ... New best solution
## ... Procrustes: rmse 0.1381199  max resid 0.3262813 
## Run 2 stress 0.02346673 
## ... New best solution
## ... Procrustes: rmse 0.1075067  max resid 0.3605672 
## Run 3 stress 0.06741553 
## Run 4 stress 0.04948565 
## Run 5 stress 0.04683001 
## Run 6 stress 0.02889005 
## Run 7 stress 0.02231042 
## ... New best solution
## ... Procrustes: rmse 0.02986127  max resid 0.09613244 
## Run 8 stress 0.05941444 
## Run 9 stress 0.02570473 
## Run 10 stress 0.07045963 
## Run 11 stress 0.05115528 
## Run 12 stress 0.04600965 
## Run 13 stress 0.04079477 
## Run 14 stress 0.05300968 
## Run 15 stress 0.0445956 
## Run 16 stress 0.06981066 
## Run 17 stress 0.06068249 
## Run 18 stress 0.0433183 
## Run 19 stress 0.02350505 
## Run 20 stress 0.04116047 
## *** No convergence -- monoMDS stopping criteria:
##      5: no. of iterations >= maxit
##     15: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Lepidoptera/Com_matrixes_data_exploration_Lepidoptera_5P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.09792603 
## Run 1 stress 0.08013479 
## ... New best solution
## ... Procrustes: rmse 0.1644326  max resid 0.3493958 
## Run 2 stress 0.05893182 
## ... New best solution
## ... Procrustes: rmse 0.1147131  max resid 0.1946275 
## Run 3 stress 0.07636956 
## Run 4 stress 0.0742606 
## Run 5 stress 0.07259878 
## Run 6 stress 0.07394452 
## Run 7 stress 0.07260071 
## Run 8 stress 0.06958962 
## Run 9 stress 0.05867092 
## ... New best solution
## ... Procrustes: rmse 0.03790794  max resid 0.1350291 
## Run 10 stress 0.08184592 
## Run 11 stress 0.04840044 
## ... New best solution
## ... Procrustes: rmse 0.0936647  max resid 0.339367 
## Run 12 stress 0.04830709 
## ... New best solution
## ... Procrustes: rmse 0.04862542  max resid 0.179496 
## Run 13 stress 0.07186128 
## Run 14 stress 0.04830893 
## ... Procrustes: rmse 0.00439486  max resid 0.01804767 
## Run 15 stress 0.07431069 
## Run 16 stress 0.06673292 
## Run 17 stress 0.06931957 
## Run 18 stress 0.08147289 
## Run 19 stress 0.06931753 
## Run 20 stress 0.0713187 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

#**END**